Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties
出版年份 2018 全文链接
标题
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties
作者
关键词
Sequence motif analysis, Macaque, Mammalian genomics, Mammals, Dogs, Animal performance, Gene expression, Polynomials
出版物
PLoS Computational Biology
Volume 14, Issue 10, Pages e1006484
出版商
Public Library of Science (PLoS)
发表日期
2018-10-05
DOI
10.1371/journal.pcbi.1006484
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
- (2016) David R. Kelley et al. GENOME RESEARCH
- DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences
- (2016) Daniel Quang et al. NUCLEIC ACIDS RESEARCH
- Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study
- (2015) John A Capra BMC GENOMICS
- Progress and challenges in bioinformatics approaches for enhancer identification
- (2015) Dimitrios Kleftogiannis et al. BRIEFINGS IN BIOINFORMATICS
- Enhancer Evolution across 20 Mammalian Species
- (2015) Diego Villar et al. CELL
- The complexity of epigenetic diseases
- (2015) Ailbhe Jane Brazel et al. JOURNAL OF PATHOLOGY
- Human Enhancers Are Fragile and Prone to Deactivating Mutations
- (2015) Shan Li et al. MOLECULAR BIOLOGY AND EVOLUTION
- Integrative analysis of 111 reference human epigenomes
- (2015) Anshul Kundaje et al. NATURE
- Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
- (2015) Babak Alipanahi et al. NATURE BIOTECHNOLOGY
- A method to predict the impact of regulatory variants from DNA sequence
- (2015) Dongwon Lee et al. NATURE GENETICS
- Predicting effects of noncoding variants with deep learning–based sequence model
- (2015) Jian Zhou et al. NATURE METHODS
- HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
- (2015) Ivan V. Kulakovskiy et al. NUCLEIC ACIDS RESEARCH
- Evolutionary changes in promoter and enhancer activity during human corticogenesis
- (2015) S. K. Reilly et al. SCIENCE
- Tissue-based map of the human proteome
- (2015) M. Uhlen et al. SCIENCE
- Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility
- (2015) Nergiz Dogan et al. Epigenetics & Chromatin
- Evidence for a common evolutionary rate in metazoan transcriptional networks
- (2015) Anne-Ruxandra Carvunis et al. eLife
- Conservation of transcription factor binding specificities across 600 million years of bilateria evolution
- (2015) Kazuhiro R Nitta et al. eLife
- Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects
- (2014) Majid Kazemian et al. Genome Biology and Evolution
- An atlas of active enhancers across human cell types and tissues
- (2014) Robin Andersson et al. NATURE
- Principles of regulatory information conservation between mouse and human
- (2014) Yong Cheng et al. NATURE
- Conservation of trans-acting circuitry during mammalian regulatory evolution
- (2014) Andrew B. Stergachis et al. NATURE
- Comparative analysis of regulatory information and circuits across distant species
- (2014) Alan P. Boyle et al. NATURE
- Evolution of transcription factor binding in metazoans — mechanisms and functional implications
- (2014) Diego Villar et al. NATURE REVIEWS GENETICS
- Transcriptional enhancers: from properties to genome-wide predictions
- (2014) Daria Shlyueva et al. NATURE REVIEWS GENETICS
- Gene Ontology Consortium: going forward
- (2014) NUCLEIC ACIDS RESEARCH
- Absence of a simple code: how transcription factors read the genome
- (2014) Matthew Slattery et al. TRENDS IN BIOCHEMICAL SCIENCES
- Enhancer variants: evaluating functions in common disease
- (2014) Olivia Corradin et al. Genome Medicine
- Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
- (2014) Mahmoud Ghandi et al. PLoS Computational Biology
- Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
- (2013) Alex S. Nord et al. CELL
- The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
- (2013) Justin Cotney et al. CELL
- Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
- (2013) Klara Stefflova et al. CELL
- Endogenous retroviruses function as species-specific enhancer elements in the placenta
- (2013) Edward B Chuong et al. NATURE GENETICS
- JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
- (2013) Anthony Mathelier et al. NUCLEIC ACIDS RESEARCH
- Ensembl 2014
- (2013) Paul Flicek et al. NUCLEIC ACIDS RESEARCH
- Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts
- (2013) C.-H. Hsu et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes
- (2012) Rita Rebollo et al. Annual Review of Genetics
- Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
- (2012) Justin Cotney et al. GENOME RESEARCH
- Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control
- (2012) G. M. Burzynski et al. GENOME RESEARCH
- Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
- (2012) D. U. Gorkin et al. GENOME RESEARCH
- Evolutionary Conservation of Histone Modifications in Mammals
- (2012) Y. H. Woo et al. MOLECULAR BIOLOGY AND EVOLUTION
- Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
- (2012) J. Merkin et al. SCIENCE
- Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
- (2012) M. T. Maurano et al. SCIENCE
- CLARE: Cracking the LAnguage of Regulatory Elements
- (2011) Leila Taher et al. BIOINFORMATICS
- TGF-β in progression of liver disease
- (2011) Steven Dooley et al. CELL AND TISSUE RESEARCH
- Discriminative prediction of mammalian enhancers from DNA sequence
- (2011) D. Lee et al. GENOME RESEARCH
- Genome-wide identification of conserved regulatory function in diverged sequences
- (2011) L. Taher et al. GENOME RESEARCH
- Embryonic Lethality and Fetal Liver Apoptosis in Mice Lacking All Three Small Maf Proteins
- (2011) H. Yamazaki et al. MOLECULAR AND CELLULAR BIOLOGY
- The evolution of gene expression levels in mammalian organs
- (2011) David Brawand et al. NATURE
- An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes
- (2010) Manonmani Arunachalam et al. BIOINFORMATICS
- Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
- (2010) Gong-Hong Wei et al. EMBO JOURNAL
- The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity
- (2010) Deborah I. Ritter et al. MOLECULAR BIOLOGY AND EVOLUTION
- Histone H3K27ac separates active from poised enhancers and predicts developmental state
- (2010) M. P. Creyghton et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
- (2010) D. Schmidt et al. SCIENCE
- A census of human transcription factors: function, expression and evolution
- (2009) Juan M. Vaquerizas et al. NATURE REVIEWS GENETICS
- Species-Specific Transcription in Mice Carrying Human Chromosome 21
- (2008) M. D. Wilson et al. SCIENCE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started